[Bioperl-l] Proposal for AI methods in Bioperl

Hilmar Lapp hlapp at gmx.net
Wed Oct 12 12:09:30 EDT 2005

You might want to look at the WEKA project for some design guidance and 
inspiration. The home page is at http://www.cs.waikato.ac.nz/ml/weka/ 
and the API is documented at http://weka.sourceforge.net/doc/

Something that's equally well structured I think could be a generally 
useful contribution. I'd expect that to use a lot of compiled code 
though, number crunching just isn't what perl is best at.

Also, it may be worth checking out the dp package in Biojava for 
dynamic programming algorithms.


On Oct 12, 2005, at 12:05 AM, Mauricio Herrera Cuadra wrote:

> Hi all,
> As far as I know, there aren't any modules in Bioperl providing access 
> to Artificial Intelligence (AI) methods such as neural networks, 
> genetic algorithms, cellular automata, among others.
> At the moment, I'm interested in developing some interface for using 
> genetic algorithms. By using the interface, users could access these 
> methods for generating optimized schemes based on sets of homologous 
> sequences. I think that the generated results could be a nice 
> alternative for motif/pattern searching in diverse novel sequences 
> (instead of regular expressions, HMM's and other methods). What do you 
> think?
> Any guidance would be really helpful. If you know of any external 
> application that you can recomend for using with the interface, a 
> suggested location in the code tree, etc., please let me know. I've 
> thought of something like a Bio::AI family that can be included in the 
> bioperl-live or maybe as a bioperl-ai package. I'm open to all kind of 
> thoughts. Thanks in advance.
> Regards,
> Mauricio.
> -- 
> arareko at campus.iztacala.unam.mx
> Laboratorio de Genética
> Unidad de Morfofisiología y Función
> Facultad de Estudios Superiores Iztacala, UNAM
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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